Merge pull request #89 from bcgov/remove-wqbc

Remove wqbc and update DOC codes

.github/workflows/R-CMD-check.yaml

@@ -1,12 +1,10 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   schedule:
     - cron:  '0 8 * * *'
 
@@ -23,88 +21,38 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@master
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@master
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - name: action-slack
         if: failure()
         env:
           SLACK_WEBHOOK_URL: ${{ secrets.POISSON_SLACK_WEBHOOK_URL }}
         uses: 8398a7/[email protected]
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          status: ${{ job.status }}
-          author_name: "github action: ${{github.workflow}}"
-          fields: repo, ref, commit, author, message
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,51 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

R/check_guidelines.R

@@ -9,7 +9,8 @@ check_guidelines <- function(x = NULL){
 
   if(is.null(x)){
     message("reading data from BC Data Catalogue ...")
-    x <-  bcdata::bcdc_get_data(record = "85d3990a-ec0a-4436-8ebd-150de3ba0747")
+    x <-  bcdata::bcdc_get_data(record = "85d3990a-ec0a-4436-8ebd-150de3ba0747", 
+                                show_col_types = FALSE)
     x <- process_limits(x)
   }
 

R/functions_data.R

@@ -25,7 +25,7 @@ process_limits <- function(limits){
                                  stringr::str_c(" (", limits$LimitNotes[limits$PC], ").")))
 
   limits$LimitNotes[limits$PC] <- limit_notes
-  limits <- dplyr::select(limits, -.data$PC)
+  limits <- dplyr::select(limits, -"PC")
 
   #### end convert background percent
 
@@ -79,11 +79,11 @@ wqg_clean <- function(data, sigfig) {
   data %>%
     dplyr::mutate(Notes = gsub("NA", "", paste(.data$ConditionNotes, .data$MethodNotes))) %>%
     dplyr::mutate(Notes = dplyr::if_else(.data$Notes == " ", NA_character_, .data$Notes)) %>%
-    dplyr::select(.data$Variable, .data$Component, Value = .data$Use, 
-                  .data$Media, .data$Type, `Predicted Effect Level` = .data$PredictedEffectLevel,
-      .data$Status, `WQG Narrative` = .data$NarrativeWQG, .data$Notes,
-      .data$Guideline, .data$Reference, .data$`Reference Link`, 
-      .data$`Overview Report Link`, .data$`Technical Document Link`)
+    dplyr::select("Variable", "Component", Value = "Use", 
+                  "Media", "Type", `Predicted Effect Level` = "PredictedEffectLevel",
+      "Status", `WQG Narrative` = "NarrativeWQG", "Notes",
+      "Guideline", "Reference", "Reference Link", 
+      "Overview Report Link", "Technical Document Link")
 }
 
 add_lookup <- function(x) {
@@ -97,7 +97,7 @@ add_lookup_condition <- function(x){
 }
 
 get_lookup_codes <- function(Limit, lookup, Condition) {
-  if(!is.null(lookup)){
+  if (!is.null(lookup)) {
       col_names <-  paste0(colnames(lookup), collapse = " ")
       lookup_parameters <- stringr::str_match_all(col_names, "EMS_.{4}")
       Condition <- paste0(lookup_parameters[[1]], sep = " ", collapse = "")
@@ -165,7 +165,11 @@ lookup_choices <- function(data, cvalue_codes){
 }
 
 get_data <- function(file_name, resource = NULL){
-  data <- try(bcdata::bcdc_get_data(record = file_name, resource = resource), silent = TRUE)
+  data <- try(bcdata::bcdc_get_data(
+    record = file_name,
+    resource = resource,
+    show_col_types = FALSE
+  ), silent = TRUE)
   if (is_try_error(data)){
     i <- file_name
     internal_data <- internal_tables[[i]]
@@ -186,6 +190,7 @@ get_data <- function(file_name, resource = NULL){
     data <- data
     data
   }
-  data
+  # TODO: Temporary workaround until CU lookup tables updated in BCDC
+  dplyr::rename(data, dplyr::any_of(c("EMS_1103" = "EMS_1126")))
 }
 

R/functions_limits.R

@@ -2,10 +2,10 @@ test_condition <- function(x, cvalues) {
   if(is.na(x))
     return (TRUE)
   # pass condition for look-up values
-  if(!stringr::str_detect(x, "[>|<|=]"))
+  if (!stringr::str_detect(x, "[>|<|=]"))
     return(TRUE)
   x <- try(eval(parse(text = x), envir = cvalues), silent = TRUE)
-  if(class(x) != "logical")
+  if(!is.logical(x))
     return (FALSE)
   if(is.na(x))
     return (FALSE)
@@ -14,7 +14,7 @@ test_condition <- function(x, cvalues) {
 
 calc_limit <- function(x, cvalues) {
   x <- try(eval(parse(text = as.character(x)), envir = cvalues), silent = TRUE)
-  if(class(x) != "numeric")
+  if (!is.numeric(x))
     return (NA)
   x
 }

R/functions_output.R

@@ -32,7 +32,7 @@ gt_table <- function(x, cvalues) {
       title = variable,
       subtitle = gt::html(cvalues)
     ) %>%
-    gt::fmt_missing(columns = gt::everything()) %>%
+    gt::sub_missing(columns = gt::everything()) %>%
     gt::cols_align(
       align = "center",
       columns = gt::everything()

R/mod_data.R

@@ -53,8 +53,10 @@ mod_data_server <- function(input, output, session) {
   observe({
 
     file_name <- "85d3990a-ec0a-4436-8ebd-150de3ba0747"
-    limit_resource <- "6f32a85b-a3d9-44c3-9a14-15175eba25b6"
-    limits <- get_data(file_name, resource = limit_resource)
+    ## TODO: Temporary workaround until CU lookup tables updated in BCDC
+    # limit_resource <- "6f32a85b-a3d9-44c3-9a14-15175eba25b6"
+    # limits <- get_data(file_name, resource = limit_resource)
+    limits <- readr::read_csv("all-wqgs-2.csv", show_col_types = FALSE)
 
     limits <- try(process_limits(limits))
     if (is_try_error(limits)) {

R/namespace.R

@@ -4,3 +4,7 @@
 #' @importFrom rlang .data
 #' @rawNamespace import(shiny, except = p)
 NULL
+
+ignore_unused_imports <- function() {
+  webshot::install_phantomjs
+}

README.Rmd

@@ -17,8 +17,8 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![img](https://img.shields.io/badge/Lifecycle-Maturing-007EC6)](https://github.com/bcgov/repomountie/blob/master/doc/lifecycle-badges.md)
-[![R-CMD-check](https://github.com/bcgov/shinywqg/workflows/R-CMD-check/badge.svg)](https://github.com/poissonconsulting/shinywqg/actions)
-[![Codecov test coverage](https://codecov.io/gh/bcgov/shinywqg/branch/master/graph/badge.svg)](https://codecov.io/gh/poissonconsulting/shinywqg?branch=master)
+[![R-CMD-check](https://github.com/bcgov/shinywqg/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bcgov/shinywqg/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/bcgov/shinywqg/branch/master/graph/badge.svg)](https://codecov.io/gh/bcgov/shinywqg?branch=master)
 [![Apache license](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 <!-- badges: end -->
 

README.md

@@ -6,9 +6,9 @@
 <!-- badges: start -->
 
 [![img](https://img.shields.io/badge/Lifecycle-Maturing-007EC6)](https://github.com/bcgov/repomountie/blob/master/doc/lifecycle-badges.md)
-[![R-CMD-check](https://github.com/bcgov/shinywqg/workflows/R-CMD-check/badge.svg)](https://github.com/poissonconsulting/shinywqg/actions)
+[![R-CMD-check](https://github.com/bcgov/shinywqg/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bcgov/shinywqg/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
-coverage](https://codecov.io/gh/bcgov/shinywqg/branch/master/graph/badge.svg)](https://codecov.io/gh/poissonconsulting/shinywqg?branch=master)
+coverage](https://codecov.io/gh/bcgov/shinywqg/branch/master/graph/badge.svg)](https://codecov.io/gh/bcgov/shinywqg?branch=master)
 [![Apache
 license](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 <!-- badges: end -->
@@ -78,9 +78,9 @@ implemented.
 Once a new version of the guidelines have been added to the BC Data
 Catalogue you will need to update the internal backup data.
 
--   Open `data-raw/internal.R`
--   Run the script from the top to bottom
--   Deploy the app
+- Open `data-raw/internal.R`
+- Run the script from the top to bottom
+- Deploy the app
 
 #### How to Add New Lookup Tables